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Loop-mediated isothermal amplification (LAMP) was developed a quarter of a century ago, but it is still not exactly clear how this reaction proceeds. Only a few articles have focused on the kinetics of LAMP and the types of products formed. In this work, 10 types were identified and named. A basic dumbbell structure, Z6_dmb(1), consists of six zones and triggers the LAMP cycle. Due to self-priming, Z6_dmb(1) transforms into hairpin structure Z9_hp(1) and then into linearized strand Z9_li(1), carrying also strand Z6_dmb(2). Through similar transformations, it again generates strand Z6_dmb(1), completing the first LAMP cycle and starting a new one. The next stage of the exponential phase starts from two Z15_hp hairpin structures generated in the LAMP cycle, which next turn into Z15_li → Z27_hp → Z27_li → Z51_hp → and so forth. Modeling of a new type of the reaction, namely, pseudo-hemi-nested LAMP (phn-LAMP), was carried out. phn-LAMP involves three inner primers: two forward (FIP and extraFIP) and one backward inner primer, or vice versa. phn-LAMP has an advantage over LAMP involving loop or stem primers and over MIP-LAMP (multiple inner primers).

Many pharmaceutical companies are avoiding the development of novel antibacterials due to a range of rational reasons and the high risk of failure. However, there is an urgent need for novel antibiotics especially against resistant bacterial strains. Available models suffer from many drawbacks and, therefore, are not applicable for scoring novel molecules with high structural diversity by their antibacterial potency. Considering this, the overall aim of this study was to develop an efficient model able to find compounds that have plenty of chances to exhibit antibacterial activity. Based on a proprietary screening campaign, we have accumulated a representative dataset of more than 140,000 molecules with antibacterial activity against assessed in the same assay and under the same conditions. This intriguing set has no analogue in the scientific literature. We applied six techniques to mine these data. For external validation, we used 5,000 compounds with low similarity towards training samples. The antibacterial activity of the selected molecules against was assessed using a comprehensive biological study. Kohonen-based nonlinear mapping was used for the first time and provided the best predictive power (av. 75.5%). Several compounds showed an outstanding antibacterial potency and were identified as translation machinery inhibitors and . For the best compounds, MIC and CC values were determined to allow us to estimate a selectivity index (SI). Many active compounds have a robust IP position.

Detection of specific RNA targets via amplification-mediated techniques is widely used in fundamental studies and medicine due to essential role of RNA in transfer of genetic information and development of diseases. Here, we report on an approach for detection of RNA targets based on the particular type of isothermal amplification, namely, reaction of nucleic acid multimerization. The proposed technique requires only a single DNA polymerase possessing reverse transcriptase, DNA-dependent DNA polymerase, and strand-displacement activities. Reaction conditions that lead to efficient detection of the target RNAs through multimerization mechanism were determined. The approach was verified by using genetic material of the SARS-CoV-2 coronavirus as a model viral RNA. Reaction of multimerization allowed to differentiate the SARS-CoV-2 RNA-positive samples from the SARS-CoV-2 negative samples with high reliability. The proposed technique allows detection of RNA even in the samples, which were subjected to multiple freezing-thawing cycles.

•SNP data are digitized as whole 4-bit boxes in the most convenient binary format.•Digitization of SNP data enables creating unique genetic identification numbers (GINs).•All SNPs used for GINs creation should be analyzed as tetra-allelic.•72 SNPs are sufficient for GINs assignment to people all over the world. Identification of individuals has become an urgent problem for mankind. In the last three decades, STR-based DNA identification has actively evolved along with traditional biometric methods. Nonetheless, single-nucleotide polymorphisms (SNPs) are now of great interest and a number of relevant SNP panels have been proposed for DNA identification. Here, a simple approach to SNP data digitization that can provide assigning a unique genetic identification number (GIN) to each person is proposed. The key points of this approach are as follows: 1) SNP data are digitized as whole 4-bit boxes in the most convenient binary format, where character “1” (YES) is assigned to revealed nucleotides, and character “0” (NO) to missing nucleotides after SNP-typing; 2) all SNPs should be considered tetra-allelic. Calculations showed that a 72-plex SNP panel is enough to provide the population with unique GINs, which can be represented in digital (binary or hexadecimal) or graphic (linear or two-dimensional) formats. Simple software for SNP data processing and GINs creation in any format was written. It is likely that the national and global GIN databases will facilitate the solution of problems related to identification of individuals or human biological materials. The proposed approach may be extended to other living organisms as well.

A series of 5-oxo-4H-pyrrolo[3,2-b]pyridine derivatives was identified as novel class of highly potent antibacterial agents during an extensive large-scale high-throughput screening (HTS) program utilizing a unique double-reporter system—pDualrep2. The construction of the reporter system allows us to perform visual inspection of the underlying mechanism of action due to two genes—Katushka2S and RFP—which encode the proteins with different imaging signatures. Antibacterial activity of the compounds was evaluated during the initial HTS round and subsequent rescreen procedure. The most active molecule demonstrated a MIC value of 3.35 µg/mL against E. coli with some signs of translation blockage (low Katushka2S signal) and no SOS response. The compound did not demonstrate cytotoxicity in standard cell viability assay. Subsequent structural morphing and follow-up synthesis may result in novel compounds with a meaningful antibacterial potency which can be reasonably regarded as an attractive starting point for further in vivo investigation and optimization.

Identification of natural donors of three bread wheat (Triticum aestivum L.) BAD subgenomes is of great importance for developing technologies aimed at improving this crop. The question about the species and subspecies of the wheat-Aegilops alliance serving as donors of the B and A subgenomes remains unanswered, while the Aegilops tauschii subspecies of strangulata is considered as a donor of the D subgenome. To identify the donor species of subgenomes of polypoid forms, the comparison of the nucleotide sequences of various genes, as well as fragments of repetitive DNA, is performed to construct phylogenetic trees. In that case, however, only one or a few genetic systems or loci are taken into analysis. The genomic barcoding proposed by the authors, which is not tied to any genetic system, has an advantage, since in silico RAPD analysis «finds» fragments matching in size in the entire genome, making, as it were, a complete «slice» of it. To estimate the phylogenetic relationship of different wheat species, we used the method of virtual multiplex RAPD analysis with 20 undecamer primers, which made it possible to create genomic barcodes of these species and compile two-dimensional maps for individual chromosomes of the analyzed wheat species. The proposed method of computer analysis of genomes showed that T. aestivum subgenome D and Ae. tauschii are very similar to each other, which may indicate their common origin. No such definite conclusions could be drawn about the donors of subgenomes A and B, which is probably due to the more ancient association of these subgenomes in tetrapioid wheat and the accumulation of a larger number of mutations over this time.